The Voynichese project provides an open-source Query Viewer and DataSets to aid researchers in the study of the Voynich Manuscript.
If you'd like to learn more about the manuscript itself, see the following resources:
http://en.wikipedia.org/wiki/Voynich_manuscript
http://www.voynich.nu/
If you're performing analysis of the manuscript and would like to use the project's enhanced transcription, see this page.
To get started with the query tool, point your browser to http://www.voynichese.com. When loaded, the application renders a grid containing 225 of the VM's folios, upon which query results are rendered.
Note that the 225 folios exclude folios f85v/f86r, also known as the Nine Rosettes page. If you'd like to study that particular folio, see the following resources:
http://brbl-zoom.library.yale.edu/viewer/1006231
https://www.jasondavies.com/voynich/#Ros2/0.501/0.501/1.00
The 225 available folios are interactive - clicking on a specific folio cell produces an enlarged version. Within the enlarged folios each individual word is also selectable. Upon selecting a given word, a query is automatically performed to highlight all of its occurrences.
Note that only exact matches are highlighted. For example, selecting the word daiin matches all occurrences of daiin exactly, excluding other words containing daiin, such as cheodaiin. To perform an inexact version of the query, ensure that the Exact option (with the 
The application's graphical user interface relies upon a collection of horizontal bars for acquiring user input, displaying information or specifying configuration settings.
At the bottom is the main character bar.
Use the character bar to assemble a query. Clicking on each character button appends or inserts the corresponding character at the active cursor position within the query input box.
Note that the asterisk is a special character that matches one or more characters - for more information see QueryBasics.
The character bar contains two additional buttons, for displaying configuration options and active queries.
Use the input bar to enter and configure a query. When then the Exact
Click the pencil button, or press enter, to render and persist the active query with a distinct color.
The input bar also displays a brief description of the query results, including the total number of word matches and a sample of the containing folios - click a folio name to locate the corresponding folio cell.
The color bar allows you to select one of the 32 supported query colors. Select a value to preview the query results using the corresponding color and click the accept button to persist the query.
The query bar lists the set of persistent queries. Persistent queries remain even as selection changes and are assigned custom colors.
The chart bar is accessible by clicking the chart button in the input bar.
The chart bar's top row displays a bar chart reflecting the distribution of the query matches throughout the 225 folios. Hover the mouse cursor over a specific column to display the number of matches within the corresponding folio - click the column to locate the folio cell.
The chart bar's bottom row lists a set of quantities detailing the query results. Use the percentage button to toggle between absolute and percentage values. For more information see the QueryResults page.
The share bar is accessible by clicking the share button in the input bar. The share bar enables you to publish a query to popular social sites and obtain minified URLs for your queries.
The options bar lists the following configuration settings.
Specifies whether an overlay should be rendered that highlights words that occur exactly once in the manuscript.
Specifies whether an overlay should be rendered that highlights words using a color scale that reflects each word's occurrence in the manuscript - the darker the color the more common the word is.
Indicates whether folio images should be rendered with high contrast. High contrast helps increase the visibility of certain folio features.
Note: currently only supported in Chrome and Safari web browsers. Indicates whether folio images should be rendered with inverted colors, resulting in a darker background color that some users may find more comfortable.
Note: currently only supported in Chrome and Safari web browsers. Specifies whether folio cells should render in color, instead of black & white. Folio cells render in monochrome by default in order to accentuate query results.
Specifies whether enlarged folios should render in color, instead of black & white.
Note: currently only supported in Chrome and Safari web browsers.